[2] After commissioning, Lincoln sailed from Baltimore on 16 September 1865 bound for Port Angeles, Washington where she arrived on 21 May 1866.

[1][2] Because the federal government needed information about the newly purchased land of Alaska, Lincoln was dispatched with orders to establish a government office, conduct surveys of the resources, produce accurate charts of the waters and locate a site for a coaling station.

During the cruise the Lincoln's crew made surveys, investigated sites for lighthouses and other aids to navigation.

[3][6] After determining that Unalaska would be an ideal site for a coaling station, Lincoln departed Alaska waters and arrived at Port Angeles on 18 November 1867 having traveled 6,297 miles (10,134 km).

[1][4] On 7 March 1868, Lincoln was ordered to San Francisco, California to exchange officers and crews with the cutter Wayanda.